Building Xcode project from Unity 'Check Dependencies' error

Hello everybody, got a bit of a problem here.

I just updated to Unity 4.3.1f1, I was previously using Unity 4.2.1f4. I'm using XCode 4.6.2 as well.

I have a post process script that builds my Xcode project, basically running a terminal command from C#. This worked fine in 4.2.1f4. However, with the new Unity I'm getting this error:
** Build Failed **
The following build commands failed:
Check dependencies
(1 failure)

This is the command I'm running:
/Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -project /Unity/iPad/Unity-iPhone.xcodeproj -configuration Debug CODE_SIGN_IDENTITY="iPhone Distribution: My Company" PROVISIONING_PROFILE="XXXXXXXXX" -arch armv7 -target "Unity-iPhone"

Now, the interesting thing is if I run that exact same command with those parameters in the terminal it works fine without any errors. Just running it from within Unity that's giving me problems. I did notice that the permissions for the Xcode project folder Unity creates are different with the new Unity. I've had to chmod the folder and its contents to be able to open it in Xcode to look at it. I've verified the profile I'm trying to sign with is valid and present.

Any help would be appreciated. Thank you!